5gio - Revision history

OCA at 11:32, 2 August 2023

2023-08-02T11:32:29Z

←Older revision		Revision as of 11:32, 2 August 2023
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	<StructureSection load='5gio' size='340' side='right'caption='[[5gio]], [[Resolution\|resolution]] 3.60Å' scene=''>		<StructureSection load='5gio' size='340' side='right'caption='[[5gio]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gio]] is a 15 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_35091 Atcc 35091~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GIO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GIO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gio]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GIO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GIO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SAH:S~~-~~ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.604Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gip\|5gip]]~~, [[~~5gin~~\|~~5gin~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>SULA_1947, SULB_1948, SULC_1946 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~2287 ATCC 35091]), rpl7ae, SULA_1106, SULB_1107, SULC_1105 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=2287 ATCC 35091]), flpA, SSOP1_0970, SULA_1948, SULB_1949, SULC_1947 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])~~</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5gio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gio OCA], [https://pdbe.org/5gio PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gio RCSB], [https://www.ebi.ac.uk/pdbsum/5gio PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gio ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5gio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gio OCA], [~~http~~://pdbe.org/5gio PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gio RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gio PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gio ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/A0A0E3JUC9_SULSF A0A0E3JUC9_SULSF]] Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA.[HAMAP-Rule:MF_00351] [[http://www.uniprot.org/uniprot/A0A0E3JZF7_SULSF A0A0E3JZF7_SULSF]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs.[HAMAP-Rule:MF_00326]	+	[https://www.uniprot.org/uniprot/Q97ZH3_SACS2 Q97ZH3_SACS2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 35091]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lin, J~~]]	+	[[Category: Saccharolobus solfataricus]]
-	[[Category: ~~Yang, Z~~]]	+	[[Category: Lin J]]
-	[[Category: ~~Ye, K~~]]	+	[[Category: Yang Z]]
-	[[Category: ~~2'-o-methylation]]~~	+	[[Category: Ye K]]
-	~~[[Category: Guide rna]]~~	+
-	~~[[Category: Rnp]]~~	+
-	~~[[Category: Transferase-rna complex~~]]	+

OCA at 06:44, 13 May 2020

2020-05-13T06:44:03Z

←Older revision		Revision as of 06:44, 13 May 2020
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	==Crystal structure of box C/D RNP with 12 nt guide regions and 13 nt substrates==		==Crystal structure of box C/D RNP with 12 nt guide regions and 13 nt substrates==
-	<StructureSection load='5gio' size='340' side='right' caption='[[5gio]], [[Resolution\|resolution]] 3.60Å' scene=''>	+	<StructureSection load='5gio' size='340' side='right'caption='[[5gio]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gio]] is a 15 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GIO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GIO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gio]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GIO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GIO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gip\|5gip]], [[5gin\|5gin]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gip\|5gip]], [[5gin\|5gin]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5gio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gio OCA], [http://pdbe.org/5gio PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gio RCSB], [http://www.ebi.ac.uk/pdbsum/5gio PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gio ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SULA_1947, SULB_1948, SULC_1946 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091]), rpl7ae, SULA_1106, SULB_1107, SULC_1105 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091]), flpA, SSOP1_0970, SULA_1948, SULB_1949, SULC_1947 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5gio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gio OCA], [http://pdbe.org/5gio PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gio RCSB], [http://www.ebi.ac.uk/pdbsum/5gio PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gio ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 35091]]
		+	[[Category: Large Structures]]
	[[Category: Lin, J]]		[[Category: Lin, J]]
	[[Category: Yang, Z]]		[[Category: Yang, Z]]

OCA at 09:49, 19 October 2016

2016-10-19T09:49:33Z

←Older revision		Revision as of 09:49, 19 October 2016
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/A0A0E3JUC9_SULSF A0A0E3JUC9_SULSF]] Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA.[HAMAP-Rule:MF_00351] [[http://www.uniprot.org/uniprot/A0A0E3JZF7_SULSF A0A0E3JZF7_SULSF]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs.[HAMAP-Rule:MF_00326]		[[http://www.uniprot.org/uniprot/A0A0E3JUC9_SULSF A0A0E3JUC9_SULSF]] Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA.[HAMAP-Rule:MF_00351] [[http://www.uniprot.org/uniprot/A0A0E3JZF7_SULSF A0A0E3JZF7_SULSF]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs.[HAMAP-Rule:MF_00326]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Box C/D RNAs guide site-specific 2'-O-methylation of RNAs in archaea and eukaryotes. The spacer regions between boxes C to D' and boxes C' to D contain the guide sequence that can form a stretch of base pairs with substrate RNAs. The lengths of spacer regions and guide-substrate duplexes are variable among C/D RNAs. In a previously determined structure of C/D ribonucleoprotein (RNP), a 12-nt-long spacer forms 10 bp with the substrate. How spacers and guide-substrate duplexes of other lengths are accommodated remains unknown. Here we analyze how the lengths of spacers and guide-substrate duplexes affect the modification activity and determine three structures of C/D RNPs assembled with different spacers and substrates. We show that the guide can only form a duplex of a maximum of 10 bp with the substrate during modification. Slightly shorter duplexes are tolerated, but longer duplexes must be unwound to fit into a capped protein channel for modification. Spacers with <12 nucleotides are defective, mainly because they cannot load the substrate in the active conformation. For spacers with >12 nucleotides, the excessive unpaired sequences near the box C/C' side are looped out. Our results provide insight into the substrate recognition mechanism of C/D RNA and refute the RNA-swapped model for dimeric C/D RNP.
		+
		+	Box C/D guide RNAs recognize a maximum of 10 nt of substrates.,Yang Z, Lin J, Ye K Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):10878-83. doi:, 10.1073/pnas.1604872113. Epub 2016 Sep 13. PMID:27625427<ref>PMID:27625427</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5gio" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:31, 14 September 2016

2016-09-14T15:31:17Z

←Older revision		Revision as of 15:31, 14 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5gio is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of box C/D RNP with 12 nt guide regions and 13 nt substrates==
-		+	<StructureSection load='5gio' size='340' side='right' caption='[[5gio]], [[Resolution\|resolution]] 3.60Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5gio]] is a 15 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GIO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GIO FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gip\|5gip]], [[5gin\|5gin]]</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5gio FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gio OCA], [http://pdbe.org/5gio PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gio RCSB], [http://www.ebi.ac.uk/pdbsum/5gio PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gio ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A0E3JUC9_SULSF A0A0E3JUC9_SULSF]] Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA.[HAMAP-Rule:MF_00351] [[http://www.uniprot.org/uniprot/A0A0E3JZF7_SULSF A0A0E3JZF7_SULSF]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs.[HAMAP-Rule:MF_00326]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lin, J]]
		+	[[Category: Yang, Z]]
		+	[[Category: Ye, K]]
		+	[[Category: 2'-o-methylation]]
		+	[[Category: Guide rna]]
		+	[[Category: Rnp]]
		+	[[Category: Transferase-rna complex]]

OCA: Protected "5gio" [edit=sysop:move=sysop]

2016-07-12T21:36:41Z

Protected "5gio" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:36, 12 July 2016

OCA: New page: '''Unreleased structure''' The entry 5gio is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2016-07-12T21:36:40Z

New page: '''Unreleased structure''' The entry 5gio is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5gio is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]